Genetic diversity,population structure and phylogenetic relationships of three indigenous pig breeds from Jiangxi Province,China, in a worldwide panel of pigs

Dongxiang Spotted, Pingxiang Two‐End‐Black and Yushan Black pigs are three indigenous breeds in Jiangxi Province, China, that have been listed in the national conservation program for Chinese indigenous livestock germplasm. Here, we investigated the genetic diversity and population structure of the nucleus populations of these three breeds in a worldwide context of European and Chinese pigs using Illumina Porcine 60K chips. Our data indicate that Dongxiang Spotted and Yushan Black pigs have recently experienced severe inbreeding. The two breeds show large runs‐of‐homozygosity values, long‐range extents of linkage disequilibrium and reduced observed heterozygosity. In contrast, Pingxiang Two‐End‐Black pigs are rich in genetic diversity and have few inbred individuals. Both phylogenetic and admixture analyses illustrate that Dongxiang Spotted and Yushan Black pigs are genetically close to their geographical neighbors in East China and that Pingxiang Two‐End‐Black pigs have a close relationship with three other Two‐End‐Black breeds in central China. Finally, we reconstructed the family structures of the three breeds and propose a reliable breeding strategy to better conserve these breeds.     

Genetic heterogeneity and selection signature at the KIT gene in pigs showing different coat colours and patterns

Mutations in the porcine KIT gene (Dominant white locus) have been shown to affect coat colours and colour distribution in pigs. We analysed this gene in several pig breeds and populations (Sicilian black, completely black or with white patches; Cinta Senese; grey local population; Large White; Duroc; Hampshire; Pietrain; wild boar; Meishan) with different coat colours and patterns, genotyping a few polymorphisms. The 21 exons and parts of the intronic regions were sequenced in these pigs and 69 polymorphisms were identified. The grey-roan coat colour observed in a local grey population was completely associated with a 4-bp deletion of intron 18 in a single copy KIT gene, providing evidence that this mutation characterizes the I^d allele described in the early genetic literature. The white patches observed in black Sicilian pigs were not completely associated with the presence of a duplicated KIT allele (I^p), suggesting that genetic heterogeneity is a possible cause of different coat colours in this breed. Selection signature was evident at the KIT gene in two different belted pig breeds, Hampshire and Cinta Senese. The same mutation(s) may cause the belted phenotype in these breeds that originated in the 18th–19th centuries from English pigs (Hampshire) and in Tuscany (Italy) in the 14th century (Cinta Senese). Phylogenetic relationships of 28 inferred KIT haplotypes indicated two clades: one of Asian origin that included Meishan and a few Sicilian black haplotypes and another of European origin.     

Acoustic communication and burrow acoustics are reflected in the ear morphology of the coruro (Spalacopus cyanus, Octodontidae), a social fossorial rodent

We studied the middle and inner ears of seven adult coruros (Spalacopus cyanus), subterranean and social rodents from central Chile, using free-hand dissection and routine staining techniques. Middle ear parameters that were focused on here (enlarged bullae and eardrums, ossicles of the "freely mobile type") are believed to enhance hearing sensitivity at lower frequencies. The organ of Corti was of a common mammalian type and revealed three peaks of higher inner hair cell densities. Based on a position frequency map, frequencies were assigned to the respective peaks along the basilar membrane. The first peak at around 300-400 Hz is discussed with respect to the burrow acoustics, while the peak around 10-20 kHz is probably a plesiomorphic feature. The most pronounced peak at around 2 kHz reflects the frequency at which the main energy of vocal communication occurs. The morphology of the ear of the coruro corresponds to the typical pattern seen in subterranean rodents (low frequency and low-sensitivity hearers), yet, at the same time, it also deviates from it in several functionally relevant features.     

Functional morphology of the ear in fossorial rodents, Microtus arvalis and Arvicola terrestris

Functionally relevant features and parameters of the outer, middle, and inner ear were studied morphologically and morphometrically in two species of voles, smaller Microtus arvalis and larger Arvicola terrestris. The findings in these fossorial (i.e., burrowing) rodents with components of surface activity were compared with respective findings reported for taxonomically related muroid rodents representing the same size classes but different eco-morphotypes: obligate subterranean rodents (Ellobius talpinus and Spalax ehrenbergi superspecies) and generalized rodents (Mus domesticus and Rattus norvegicus). The ear in voles was characterized by traits reported for subterranean rodents. The eardrum was round, without a distinct pars flaccida, and had an area of 5.4 mm2 in M. arvalis and 9 mm2 in A. terrestris. The middle ear exhibited reduced goniale, enlarged incus nearly parallel to the manubrium of the malleus. The malleus-incus lever ratio amounted to 2.1 (M. arvalis) and 2.0 (A. terrestris). The malleus-incus complex weighed about 0.8 mg in both vole species. The stapedial footplate had an area of 0.3 mm2 in M. arvalis and 0.4 mm2 in A. terrestris. The cochlea had 2.3 coils in both vole species; the basilar membrane was 8.5 mm and 10.5 mm long in M. arvalis and A. terrestris, respectively. There were on average 1,030 (M. arvalis) and 1,220 (A. terrestris) inner hair cells, and 3,760 (M. arvalis) and 4,250 (A. terrestris) outer hair cells in the organ of Corti. In quantitative terms, all these (as well as some further) traits and parameters were intermediate (related to body size) between those reported for generalized rodents on the one hand and subterranean ones on the other. The sound transmission system of the ear seems to be best tuned to frequencies of about 8-16 kHz with a high-frequency cut-off at about 50-60 kHz. The ear of A. terrestris seems to be tuned to somewhat lower frequencies than that in M. arvalis. In this aspect as well as regarding hearing sensitivity (as judged from the mechanical transmission parameters), voles can be considered intermediate not only in their lifestyle but also in their hearing abilities between the subterranean rodents (mole-vole and blind mole-rat) and the surface dwellers (house mouse and Norway rat).     

Genetic resources of wild barley in the Near East: structure, evolution and application in breeding

Genetic diversity and structure of populations of the wild progenitor of barley, Hordeum spontaneum, from three countries, Israel, Turkey and Iran, in the Near East Fertile Crescent, are compared and contrasted. The analysis is based on electrophoretically discernible allozymic variation in proteins encoded by 27 shared loci in 2125 individuals representing 52 populations of wild barley. The results indicate that: (a) H. spontaneum in the Near East Fertile Crescent is very variable genetically; (b) genetic differentiation of populations includes some clinal but primarily regional and local patterns often displaying sharp geographic differentiation over short distances; (c) the average relative genetic differentiation (G_st) was 54% within populations, 39% among populations, and 8% between the three countries; (d) allele distribution is characterized by a high proportion of unique alleles (51%), and a high proportion of common alleles that are distributed either locally or sporadically; (e) discriminant analysis by allele frequencies successfully clustered wild barley of each of the three countries (96% correct classification); (f) a substantial portion of the patterns of allozyme variation in the wild gene pool is significantly correlated with the environment and is predictable ecologically, chiefly by a combination of humidity and temperature variables; (g) natural populations of wild barley are, on the average, more variable than two composite crosses and land races of cultivated barley. The spatial patterns and environmental correlates and predictors of genetic variation of H, spontaneum in the Fertile Crescent indicate that genetic variation in wild barley populations is not only rich but at least partly adaptive and predictable by ecology and allozyme markers. Consequently, conservation and utilization programmes should optimize sampling strategies by following the ecological-genetic factors and allozyme markers as effectively predictive guidelines.     

Novel seed coat lignins in the Cactaceae: structure,distribution and implications for the evolution of lignin diversity

We have recently described a hitherto unsuspected catechyl lignin polymer (C‐lignin) in the seed coats of Vanilla orchid and in cacti of one genus, Melocactus (Chen et al., Proc. Natl. Acad. Sci. USA. 2012, 109, 1772‐1777.). We have now determined the lignin types in the seed coats of 130 different cactus species. Lignin in the vegetative tissues of cacti is of the normal guaiacyl/syringyl (G/S) type, but members of most genera within the subfamily Cactoidae possess seed coat lignin of the novel C‐type only, which we show is a homopolymer formed by endwise β–O–4‐coupling of caffeyl alcohol monomers onto the growing polymer resulting in benzodioxane units. However, the species examined within the genera Coryphantha, Cumarinia, Escobaria and Mammillaria (Cactoideae) mostly had normal G/S lignin in their seeds, as did all six species in the subfamily Opuntioidae that were examined. Seed coat lignin composition is still evolving in the Cactaceae, as seeds of one Mammillaria species (M. lasiacantha) possess only C‐lignin, three Escobaria species (E. dasyacantha, E. lloydii and E. zilziana) contain an unusual lignin composed of 5‐hydroxyguaiacyl units, the first report of such a polymer that occurs naturally in plants, and seeds of some species contain no lignin at all. We discuss the implications of these findings for the mechanisms that underlie the biosynthesis of these newly discovered lignin types.     

The distribution, natural habitats and availability of wild cereals in relation to their domestication in the Near East: multiple events, multiple centres

In this article we examine the natural habitats and distribution of the six wild cereals: Triticum urartu (wild urartu wheat), T. boeoticum aegilopoides (single-grained wild einkorn), T. boeoticum thaoudar (two-grained wild einkorn), T. dicoccoides (wild emmer wheat), Secale spp. (wild ryes) and Hordeum spontaneum (wild barley). A comparison of late Pleistocene/early Holocene archaeobotanical assemblages in the Near East with present-day distributions of wild cereals shows a good correlation. The regional variation in the archaeobotanical cereal assemblages and the ensuing domestication provide evidence that different cereal species were domesticated independently in different areas. Some sites were not situated near wild cereal habitats and a few were located outside the limits of distribution, even accounting for moister climatic conditions. I argue here that current models which try to explain the shift to farming have tended to over-emphasize the effect of the Younger Dryas climatic change. First, it would have had only a minor effect on cereal availability. Secondly, agriculture appears to have been established after the Younger Dryas. Thirdly, there is no evidence for a single centre of origin; agriculture arose in widely separated geographic and climatic regions. And fourthly, agriculture depends on stable climatic conditions which were not established until after the Younger Dryas.     

Effect of fibre sources on performance,serum parameters,intestinal morphology,digestive enzyme activities and microbiota in weaned pigs

ABSTRACT

This study was conducted to evaluate the effects of wheat bran (WB) as insoluble fibre source, and sugar beet pulp (SBP) as soluble fibre source, on performance, serum parameters and intestinal health in weaned pigs. A total of 90 weaned pigs (BW: 7.33 ± 1.24 kg) were randomly assigned to three dietary treatments: (1) a control diet (CON) based on corn and soybean meal; (2) CON + 6% WB; (3) CON + 6% SBP. Each treatment had five replicate pens with six pigs per pen. The experimental period was divided into two phases (d 0 to 14 and d 14 to 28). Pigs in group WB tended to have greater avarage daily gain than those in group SBP. Compared with CON, SBP reduced (p < 0.05) the apparent total tract digestibility (ATTD) of dry matter, organic matter (OM), gross energy and neutral detergent fibre on d 14 and 28, while WB decreased (p < 0.05) the ATTD of OM on d 28. Pigs in group SBP had higher (p < 0.05) glucagon-like peptide 1 concentration than the other groups on d 14 and 28. The villus height to crypt depth (V:C) ratio of duodenum and jejunum in pigs fed diet WB were greater (p < 0.05) than in group SBP. The WB increased (p < 0.05) the V:C ratio of ileum compared with CON or SBP. Compared with SBP, WB increased (p < 0.05) the sucrase activity in the duodenum. Moreover, pigs in WB had higher (p < 0.05) activities of maltase and sucrase in the jejunum compared with CON or SBP. The abundances of Ruminococcaceae and Prevotellaceae were increased (p < 0.05) in WB, while the Lachnospiraceae abundance was increased (p < 0.05) in SBP. WB increased (p < 0.05) concentrations of acetate, butyrate and total short-chain fatty acids (SCFA), while SBP increased (p < 0.05) concentrations of acetate and total SCFA when compared with CON. In conclusion, WB was beneficial to performance in weaned pigs by improving morphology, enzyme activities and microbiota when compared with SBP, highlighting that effects of fibre depends on the fibre sources.     

Recognition of foreignness by blood cells of the freshwater snail Lymnaea stagnalis, with special reference to the role and structure of the cell coat

The structure and function of the cell coat of the blood cells (amoebocytes) of the freshwater snail Lymnaea stagnalis were studied with ultrahistochemical tests, including concanavalin A (Con A) labeling, and with in vitro phagocytosis experiments. The cell coat is intensely stained by ruthenium red and tannic acid. The cells possess binding sites for Con A. Proteolytic enzymes destroy the receptors for Con A and totally inhibit the phagocytic activity of amoebocytes. Incubation experiments with proteases, carbohydrases, and inhibition sugars revealed that (1) the Con A binding sites are anchored in the plasma membrane by proteins, and (2) glucose, fructose, mannose, and to a lesser extent N-acetylglucosamine and N-acetylgalactosamine, inhibit the binding of Con A to amoebocytes, suggesting that these carbohydrates might form part of these binding sites.     

Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences

Portunus trituberculatus is a commercially important fishery species. In this study, intraspecific variation was examined by using mitochondrial DNA 16S rRNA gene in 213 individual crabs sampled from six localities along the coast of the East China Sea. Twenty-two polymorphic sites defined 25 distinct haplotypes, revealing a moderately high haplotype diversity and relatively low sequence divergence among the six localities. An excess of within population unique haplotypes at most sample locations were detected, which might influence genetic structure of the swimming crab populations. Neither neighbor-joining tree nor minimum spanning network (MSN) based on the haplotype data indicated distinct patterns of phylogeographic structure among the 25 haplotypes. Analyses of molecular variance (AMOVA) and F_ST statistics supported the hypothesis that population samples from the East China Sea were genetically nonhomogenous, indicating that gene flow might be restricted across those regions, despite the high potential of dispersal. In addition, tests of neutral evolution and analysis of mismatch distribution suggested that P. trituberculatus might have undergone a population expansion, possibly within the last 127,000 and 429,000 years. Our study unraveled the extant population genetic structure of the P. trituberculatus, and addressed the related fishery management issues including artificial breeding, fishery stock identification and conservation.     

春季东海海域虾类群落结构及其多样性

依据1998年5月(春季)在东海26°00′N～33°00′N、127°00′E以西海域的虾类资源调查资料,分析了虾类的种类组成、优势度、丰度、生物量的空间分布,多样性、相似性等群落结构特征.结果表明,东海大陆架春季共有虾类52种,已鉴定的43种,隶属于13科27属,其中优势种有戴氏赤虾(Metapenaepsis dalei)、假长缝拟对虾(Parapenaeus fissuroides)、须赤虾(Metapenaepsis barbata)、葛氏长臂虾(Palaemon gravieri)、中华管鞭虾(Solenocera crassicornis)、东海红虾(Plesionika izumiae)、鹰爪虾(Trachypenaeus curvirostris)、方板赤虾(Metapenaepsis tenella)、长角赤虾 Metapenaepsis longirostris、高脊管鞭虾(Solenocera alticarinata)、细巧仿对虾(Parapenaeopsis tenella)、周氏新对虾(Metapenaeus joyneri)、脊腹褐虾(Crangon affinis)和凹管鞭虾(Solenocera koellbeli).东海大陆架春季虾类可划分为3个生态群落,即广温低盐生态群落、广温广盐生态群落、高温高盐生态群落.丰度和生物量的平面分布趋势相似,以30°00′N为界限,30°00′N以北站位普遍较低,以南站位较高,主要集中在舟山渔场南部和鱼山渔场.多样性分析表明:Margalef的种类丰富度指数(D)和Shannon-Wiener多样性指数(H′)较高的站位主要集中在舟山渔场以北,整个海区的均匀性指数(J′)较为稳定.运用聚类和多维标度对群落结构的相似性进行分析,结合水深等环境因子对东海大陆架虾类的群聚类型进行了讨论.     

The Early Stone Age lithic assemblages of Gadeb (Ethiopia) and the Developed Oldowan/early Acheulean in East Africa

The Early Stone Age sites of Gadeb (Ethiopian South-East Plateau) were excavated under the direction of Desmond Clark in the 1970s. Dated to between 1.45 and 0.7 Ma, Gadeb proved that humans had already occupied high altitude areas in the Lower Pleistocene. Despite the importance of the Gadeb sites, their lithic assemblages were never published in detail, and no review of the stone tools has ever been reported since the original 1970s study. This paper updates the information available on Gadeb by presenting a systematic review of the lithic technology of several assemblages. The objectives are to evaluate the technological skills of Gadeb knappers and to contextualize them into the current discussion of the origins of the Acheulean and its possible coexistence with the so-called Developed Oldowan in East Africa.     

Digestive gut structure and activity of protease, amylase, and alkaline phosphatase in Calanus sinicus during summer in the Yellow Sea and the East China Sea

Calanus sinicus aggregate at the depth of 40–60 m (ambient temperature is 16 °C) in the waters of the continental shelf of the Yellow Sea during summer. In animals found in near shore regions, there are changes in digestive gut cells structure, digestive enzyme activity (protease, amylase), and tissue enzyme (alkaline phosphatase (ALP)), which may represent adaptations by this cold-water animal to a sharp seasonal increase in temperature of 6–23 °C. The activities of the digestive enzymes (protease and amylase) are very low in animals at stations near the estuary of Yangtse River, whereas they are relatively high in animals at stations in the central Yellow Sea. During summer, B-cells of the intestine and the villi intestinalis disappear in animals that do not feed at stations near the estuary of the Yangtse River. Respiration rates were undetectable or quite low during summer in C. sinicus from stations near the estuary of the Yangtse River, whereas they were relatively high at stations in the central Yellow Sea. Based upon the morphological characteristics of the digestive gut structure, enzyme levels, respiration rates, and the distribution of C. sinicus, we concluded that C. sinicus might be dormant during summer in the near shore areas of the East China Sea while remaining active in the central Yellow Sea.     

Composition,ultrastructure and function of the cutin- and suberin-containing layers in the leaf,fruit peel,juice-sac and inner seed coat of grapefruit (Citrus paradisi Macfed.)

Cutin and suberin polymers from various anatomical regions of grapefruit were analyzed chemically and ultrastructurally. The leaf, fruit peel and juice-sac showed an amorphous cuticular layer. The cutin in the leaf was composed of 10,16-dihydroxy C₁₆ acid and its positional isomers as the major monomers whereas 16-hydroxy-10-oxo C₁₆ acid was a major component in the fruit peel. Juice-sac cutin, on the other hand, contained the dihydroxy C₁₆ acids, hydroxyoxo C₁₆ acids, hydroxyepoxy C₁₈ acids and trihydroxy C₁₈ acids. Ultrastructural examination of the inner seed coat showed that an amorphous cuticular layer encircled the entire seed except in the chalazal region which showed several layers of cells with lamellar suberin structure throughout the cell walls. Consistent with the ultrastructural assignment, the compositions of the aliphatic components of the polymers from the chalazal region and the non-chalazal region indicated the presence of suberin and cutin, respectively. The aliphatic portion of the polymer from the chalazal region of the inner seed coat contained C₁₆, C_18:1, C₂₂ and C₂₄ -hydroxy acids (46% combined total) and the corresponding dicarboxylic acids (43%) as the major components. -Hydroxy-9,10-epoxy C₁₈ acids and 9,10,18-trihydroxy C₁₈ acids were the major components (77%) of the polymer from the non-chalazal portion of the inner seed coat. The main portion and the chalazal region of the inner seed coat yielded 17 and 342 g/cm² of aliphatic monomers, respectively, and the diffusion resistance of these two portions of the inner seed coat were 62 and 192 sec/cm, respectively. The inner seed coat was shown to be the major moisture diffusion barrier influencing imbibition and germination.Scientific Paper No. 5649, Project 2001, College of Agriculture Research Center, Washington State University, Pullman, Washington 99164     

The biology of stone loach Barbatula barbatulus in the Rivers Goloustnaya and Olkha, East Siberia

Five hundred and four stone loach 63–202 mm in total length, of I + to 8 + age groups, were sampled in two rivers of East Siberia from April to October 1989–90. This paper presents data on the seasonal dynamics of fecundity, ripening, fatness and feeding intensity. A second spawning from the end of August to October has been identified for the first time for this species. The absolute fecundity ranged from 1710 to 27600, and the relative fecundity varied from 216 to 833 eggs g⁻¹: (fish weight). Stone loach in the River Olkha grew faster than those in the River Goloustnaya and, according to this index, are closer to stone loach from streams of northern England.     

Investigations into seed dormancy in Grevillea linearifolia, G. buxifolia and G. sericea: anatomy and histochemistry of the seed coat

BACKGROUND AND AIMS: Seeds of east Australian Grevillea species generally recruit post-fire; previous work showed that the seed coat was the controller of dormancy in Grevillea linearifolia. Former studies on seed development in Grevillea have concentrated on embryology, with little information that would allow testing of hypotheses about the breaking of dormancy by fire-related cues. Our aim was to investigate structural and chemical characteristics of the seed coat that may be related to dormancy for three Grevillea species. METHODS: Seeds of Grevillea linearifolia, Grevillea buxifolia and Grevillea sericea were investigated using gross dissection, thin sectioning and histochemical staining. Water movement across the seed coat was tested for by determining the water content of embryos from imbibed and dry seeds of G. sericea. Penetration of intact seeds by Lucifer Yellow was used to test for internal barriers to diffusion of high-molecular-weight compounds. KEY RESULTS: Two integuments were present in the seed coat: an outer testa, with exo-, meso- and endotestal (palisade) layers, and an inner tegmen of unlignified sclerenchyma. A hypostase at the chalazal end was a region of structural difference in the seed coat, and differed slightly among the three species. An internal cuticle was found on each side of the sclerenchyma layer. The embryos of imbibed seeds had a water content six times that of dry seeds. Barriers to diffusion of Lucifer Yellow existed at the exotestal and the endotestal/hypostase layers. CONCLUSIONS: Several potential mechanisms of seed coat dormancy were identified. The embryo appeared to be completely surrounded by outer and inner barriers to diffusion of high-molecular-weight compounds. Phenolic compounds present in the exotesta could interfere with gas exchange. The sclerenchyma layer, together with strengthening in the endotestal and exotestal cells, could act as a mechanical constraint.